| 3vfzA |
| ID: | 1385744236 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (69) | ||
| Sequences: | 3450 (2892.9) | ||
| Seq/Len: | 50.000 | ||
| Nf(neff/√len): | 348.3 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 50.000).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 43_R | 53_T | 2.908 | 1.00 |
| 51_E | 61_T | 2.438 | 1.00 |
| 48_L | 56_A | 2.381 | 1.00 |
| 36_Q | 74_R | 2.229 | 1.00 |
| 31_I | 78_E | 2.033 | 1.00 |
| 60_T | 63_A | 1.943 | 1.00 |
| 35_K | 67_A | 1.891 | 1.00 |
| 28_L | 78_E | 1.845 | 1.00 |
| 62_G | 65_R | 1.744 | 1.00 |
| 63_A | 66_V | 1.742 | 1.00 |
| 63_A | 67_A | 1.672 | 1.00 |
| 33_P | 36_Q | 1.590 | 1.00 |
| 37_R | 41_I | 1.589 | 1.00 |
| 44_V | 72_L | 1.572 | 1.00 |
| 39_I | 68_Q | 1.571 | 1.00 |
| 68_Q | 72_L | 1.528 | 1.00 |
| 59_S | 67_A | 1.505 | 1.00 |
| 66_V | 69_H | 1.397 | 0.99 |
| 43_R | 50_A | 1.385 | 0.99 |
| 42_L | 56_A | 1.384 | 0.99 |
| 50_A | 61_T | 1.364 | 0.99 |
| 50_A | 68_Q | 1.302 | 0.99 |
| 39_I | 71_A | 1.301 | 0.99 |
| 36_Q | 67_A | 1.240 | 0.98 |
| 62_G | 69_H | 1.209 | 0.98 |
| 50_A | 65_R | 1.207 | 0.98 |
| 30_E | 37_R | 1.202 | 0.98 |
| 53_T | 64_V | 1.187 | 0.98 |
| 62_G | 66_V | 1.168 | 0.97 |
| 36_Q | 70_R | 1.159 | 0.97 |
| 39_I | 59_S | 1.123 | 0.97 |
| 61_T | 65_R | 1.119 | 0.96 |
| 69_H | 73_Q | 1.117 | 0.96 |
| 42_L | 53_T | 1.107 | 0.96 |
| 44_V | 68_Q | 1.067 | 0.95 |
| 20_D | 23_T | 1.064 | 0.95 |
| 49_S | 52_E | 1.061 | 0.95 |
| 59_S | 63_A | 1.060 | 0.95 |
| 42_L | 57_V | 1.048 | 0.94 |
| 34_A | 38_E | 1.029 | 0.94 |
| 51_E | 55_A | 1.016 | 0.93 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3vdoA | 1 | 0.7326 | 99.3 | 0.192 | Contact Map |
| 3vfzA | 2 | 0.7326 | 99.3 | 0.194 | Contact Map |
| 1or7A | 2 | 0.8837 | 99.3 | 0.194 | Contact Map |
| 2q1zA | 2 | 0.9186 | 99.3 | 0.195 | Contact Map |
| 3hugA | 10 | 0.9302 | 99.2 | 0.204 | Contact Map |
| 2lfwA | 1 | 0.9884 | 99.2 | 0.216 | Contact Map |
| 1rp3A | 4 | 0.9651 | 99.2 | 0.221 | Contact Map |
| 3mzyA | 1 | 0.8488 | 99.2 | 0.224 | Contact Map |
| 1l0oC | 1 | 0.0349 | 99.1 | 0.248 | Contact Map |
| 4ljzF | 2 | 1 | 99.1 | 0.251 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)